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Identification
YMDB IDYMDB00330
NameL-Lysine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionLysine (abbreviated as Lys or K) is an alpha-amino acid. The L-isomer is one of the 22 proteinogenic amino acids, i.e., the building blocks of proteins. It is classified as a polar, basic amino acid, because of the positively charged nature of the amino-alkyl side chain. In yeast, lysine is synthesized from aspartic acid (aspartate). Specifically, L-aspartate is first converted to L-aspartyl-4-phosphate by aspartokinase (or Aspartate kinase). Subsequently, beta-aspartate semialdehyde dehydrogenase converts this into beta-aspartyl-4-semialdehyde (or beta-aspartate-4-semialdehyde) through an NADH-dependent reaction. After this step, Dihydrodipicolinate synthase adds a pyruvate group to the beta-aspartyl-4-semialdehyde, and two water molecules are removed. This causes cyclization and gives rise to 2,3-dihydrodipicolinate. This product is reduced to 2,3,4,5-tetrahydrodipicolinate by dihydrodipicolinate reductase. Tetrahydrodipicolinate N-acetyltransferase opens this ring and gives rise to N-succinyl-L-2-amino-6-oxoheptanedionate (or N-acyl-2-amino-6-oxopimelate). N-succinyl-L-2-amino-6-oxoheptanedionate is converted into N-succinyl-LL-2,6-diaminoheptanedionate (N-acyl-2,6-diaminopimelate). This reaction is catalyzed by the enzyme succinyl diaminopimelate aminotransferase. A glutaric acid molecule is used in this reaction and an oxoacid is produced as a byproduct. N-succinyl-LL-2,6-diaminoheptanedionate (N-acyl-2,6-diaminopimelate)is converted into LL-2,6-diaminoheptanedionate (L,L-2,6-diaminopimelate) by succinyl diaminopimelate desuccinylase (acyldiaminopimelate deacylase). A water molecule is consumed in this reaction and a succinate is produced a byproduct. LL-2,6-diaminoheptanedionate is converted by diaminopimelate epimerase into meso-2,6-diamino-heptanedionate (meso-2,6-diaminopimelate). Finally meso-2,6-diamino-heptanedionate is converted into L-lysine by diaminopimelate decarboxylase. Lysine catabolism is unusual in the way that the ε-amino group is transferred to alpha-ketoglutarate and into the general nitrogen pool. The reaction is a transamination in which the ε-amino group is transferred to the alpha-keto carbon of alpha-ketoglutarate forming the metabolite, saccharopine. Saccharopine is immediately hydrolyzed by the enzyme alpha-aminoadipic semialdehyde synthase in such a way that the amino nitrogen remains with the alpha-carbon of alpha-ketoglutarate, producing glutamate and alpha-aminoadipic semialdehyde. The ultimate end-product of lysine catabolism is acetoacetyl-CoA.
Structure
Thumb
Synonyms
  • (+)-S-Lysine
  • (S)-2,6-diamino-Hexanoate
  • (S)-2,6-diamino-Hexanoic acid
  • (S)-2,6-Diaminohexanoate
  • (S)-2,6-Diaminohexanoic acid
  • (S)-a,e-Diaminocaproate
  • (S)-a,e-Diaminocaproic acid
  • (S)-Lysine
  • 2,6-Diaminohexanoate
  • 2,6-Diaminohexanoic acid
  • 6-amino-Aminutrin
  • 6-amino-L-Norleucine
  • a-Lysine
  • alpha-Lysine
  • Aminutrin
  • h-Lys-oh
  • L-(+)-Lysine
  • L-2,6-Diainohexanoate
  • L-2,6-Diainohexanoic acid
  • L-2,6-Diaminocaproate
  • L-2,6-Diaminocaproic acid
  • L-Lys
  • Lys
  • Lysine
  • Lysine acid
  • (S)-alpha,epsilon-Diaminocaproic acid
  • 6-Ammonio-L-norleucine
  • K
  • L-Lysin
  • Lysina
  • Lysinum
  • (S)-a,epsilon-Diaminocaproate
  • (S)-a,epsilon-Diaminocaproic acid
  • (S)-alpha,epsilon-Diaminocaproate
  • (S)-Α,epsilon-diaminocaproate
  • (S)-Α,epsilon-diaminocaproic acid
  • Acetate, lysine
  • Enisyl
  • Lysine hydrochloride
  • L Lysine
  • Lysine acetate
CAS number56-87-1
WeightAverage: 146.1876
Monoisotopic: 146.105527702
InChI KeyKDXKERNSBIXSRK-YFKPBYRVSA-N
InChIInChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m0/s1
IUPAC Name(2S)-2,6-diaminohexanoic acid
Traditional IUPAC NameL-lysine
Chemical FormulaC6H14N2O2
SMILES[H]OC(=O)[C@@]([H])(N([H])[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])N([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentL-alpha-amino acids
Alternative Parents
Substituents
  • L-alpha-amino acid
  • Medium-chain fatty acid
  • Amino fatty acid
  • Fatty acid
  • Fatty acyl
  • Amino acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Organic nitrogen compound
  • Amine
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point224.5 °C
Experimental Properties
PropertyValueReference
Water Solubility1000 mg/mL at 20 oC [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
LogP-3.05 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility105 g/LALOGPS
logP-3.8ALOGPS
logP-3.2ChemAxon
logS-0.14ALOGPS
pKa (Strongest Acidic)2.74ChemAxon
pKa (Strongest Basic)10.29ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area89.34 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity37.81 m³·mol⁻¹ChemAxon
Polarizability15.84 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
  • mitochondrion
  • vacuole
  • cytoplasm
Organoleptic Properties
Flavour/OdourSource
OdorlessFDB000474
SMPDB Pathways
lysine metabolismPW002420 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Biotin metabolismec00780 Map00780
Lysine biosynthesisec00300 Map00300
Lysine degradationec00310 Map00310
SMPDB Reactions
Saccharopine + NAD + waterNADH + hydron + Oxoglutaric acid + L-Lysine
KEGG Reactions
Adenosine triphosphate + tRNA(Lys) + L-LysineAdenosine monophosphate + Pyrophosphate + Lys-tRNA(Lys)
NAD + water + SaccharopineNADH + Oxoglutaric acid + hydron + L-Lysine
Concentrations
Intracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
702 ± 14 µM YPD mediaaerobicBaker's yeastPMID: 7654310
561 ± 11 µM YPG mediaaerobicBaker's yeastPMID: 7654310
351 ± 7 µM SD mediaaerobicBaker's yeastPMID: 7654310
421 ± 8 µM SG mediaaerobicBaker's yeastPMID: 7654310
351 ± 7 µM M (molasses)aerobicBaker's yeastPMID: 7654310
842 ± 17 µM MA (molasses)aerobicBaker's yeastPMID: 7654310
281 ± 6 µM MB (molasses)aerobicBaker's yeastPMID: 7654310
772 ± 15 µM MAB (molasses)aerobicBaker's yeastPMID: 7654310
3620 ± 181 µM YEB media with 0.5 mM glucoseaerobicBaker's yeastExperimentally Determined
Not Available
1860 ± 683 µM Synthetic medium with 20 g/L glucoseaerobicBaker's yeastPMID: 12584756
Conversion Details Here
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)splash10-00di-3910000000-98c565675de67aa87900JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0ab9-1910000000-87ef8534f592041f50f2JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0a4i-1921000000-84f7815b0f650fa17444JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-001i-9600000000-823408dba509cb204acfJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-00di-3910000000-4f5578af5e7d8b6c49f7JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (4 TMS)splash10-0adi-1921000000-4e56d95e623e792f9e6bJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-00di-0921000000-eeb49e57bc1a75193058JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0ab9-0921000000-ebb902be0f3754225b2fJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-3910000000-98c565675de67aa87900JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0ab9-1910000000-87ef8534f592041f50f2JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-QQ (Non-derivatized)splash10-0fdk-3923000000-15b84c2649c1b0455de1JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0a4i-1921000000-84f7815b0f650fa17444JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-001i-9600000000-823408dba509cb204acfJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-00di-3910000000-4f5578af5e7d8b6c49f7JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0adi-1921000000-4e56d95e623e792f9e6bJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0abi-1900000000-9ad174122e4d6e003eb8JSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0089-9100000000-974cc55c9130ed5213ebJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0ue9-9700000000-57b24ae819b6ec26bfd2JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-003r-8900000000-470a0beb4f338ed89bcaJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-001i-9000000000-74e9193d9d33c2509bfaJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0a59-9000000000-822c4e78250fffa56e39JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0002-0900000000-04f9a62a77fb5a37ca22JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-001i-9000000000-035035ecfa084671479bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-001i-0900000000-5bb15839f86f4fca0d0bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-001i-0900000000-6c8ef03aa83eb1cab35bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-01ot-0910000000-c182a7dcdbc260666978JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0a4j-0900000000-6c5f378cef2f14204e15JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-001i-0900000000-41e1a6499097748934b0JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-03di-0390000000-7270a0b85b9e3f9f6373JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-0002-0900000000-a997e809874357908880JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0002-2900000000-f64110414f82c93e1fe8JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-014m-9200000000-33a38e6370811c5ddc82JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0006-9000000000-3a8b0b6e62f5c66d3720JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0006-9000000000-d5167570d11d77fd541eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-0002-0900000000-a46231bd529176101129JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-001i-9200000000-f8b9f01b2a9886c51df9JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-001i-9000000000-ace0361476d939043e98JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-001i-9000000000-5b06b6e9dcf9faf8e89cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-053r-9000000000-2894ef6d7f72ea71688eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - CE-ESI-TOF (CE-system connected to 6210 Time-of-Flight MS, Agilent) , Positivesplash10-0002-0900000000-290902f43cf851e8ef5eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-001i-9300000000-f81193f6b50235ec8147JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-001i-9300000000-8931d2193adab166d5e4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-0002-0900000000-b4825cc64fcb830c6967JSpectraViewer | MoNA
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • Martinez-Force, E., Benitez, T. (1995). "Effects of varying media, temperature, and growth rates on the intracellular concentrations of yeast amino acids." Biotechnol Prog 11:386-392.7654310
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Arevalo-Rodriguez, M., Calderon, I. L., Holmberg, S. (1999). "Mutations that cause threonine sensitivity identify catalytic and regulatory regions of the aspartate kinase of Saccharomyces cerevisiae." Yeast 15:1331-1345.10509015
  • Hans, M. A., Heinzle, E., Wittmann, C. (2003). "Free intracellular amino acid pools during autonomous oscillations in Saccharomyces cerevisiae." Biotechnol Bioeng 82:143-151.12584756
  • Castrillo, J. I., Zeef, L. A., Hoyle, D. C., Zhang, N., Hayes, A., Gardner, D. C., Cornell, M. J., Petty, J., Hakes, L., Wardleworth, L., Rash, B., Brown, M., Dunn, W. B., Broadhurst, D., O'Donoghue, K., Hester, S. S., Dunkley, T. P., Hart, S. R., Swainston, N., Li, P., Gaskell, S. J., Paton, N. W., Lilley, K. S., Kell, D. B., Oliver, S. G. (2007). "Growth control of the eukaryote cell: a systems biology study in yeast." J Biol 6:4.17439666
Synthesis Reference:Rothstein, Morton. DL-Lysine-6-C14 and DL-a-aminoadipic acid-6-C14. Biochemical Preparations (1961), 8 85-8.
External Links:
ResourceLink
CHEBI ID18019
HMDB IDHMDB00182
Pubchem Compound ID5962
Kegg IDC00047
ChemSpider ID5747
FOODB IDFDB000474
WikipediaLysine
BioCyc IDLYS

Enzymes

General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the NAD(+)-dependent cleavage of saccharopine to L-lysine and 2-oxoglutarate
Gene Name:
LYS1
Uniprot ID:
P38998
Molecular weight:
41464.39844
Reactions
N(6)-(L-1,3-dicarboxypropyl)-L-lysine + NAD(+) + H(2)O → L-lysine + 2-oxoglutarate + NADH.
General function:
Involved in nucleotide binding
Specific function:
ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys)
Gene Name:
MSK1
Uniprot ID:
P32048
Molecular weight:
66127.60156
Reactions
ATP + L-lysine + tRNA(Lys) → AMP + diphosphate + L-lysyl-tRNA(Lys).
General function:
Involved in nucleotide binding
Specific function:
ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys)
Gene Name:
KRS1
Uniprot ID:
P15180
Molecular weight:
67958.0
Reactions
ATP + L-lysine + tRNA(Lys) → AMP + diphosphate + L-lysyl-tRNA(Lys).

Transporters

General function:
Involved in transport
Specific function:
Permease for various amino acids as well as for GABA. Can also transport L-cysteine and beta-alanine
Gene Name:
GAP1
Uniprot ID:
P19145
Molecular weight:
65654.89844
General function:
Involved in transmembrane transport
Specific function:
Transporter required for vacuolar uptake of at least histidine and lysine
Gene Name:
VBA1
Uniprot ID:
Q04301
Molecular weight:
62638.80078
General function:
Involved in transmembrane transport
Specific function:
Transporter required for vacuolar uptake of histidine and lysine
Gene Name:
VBA3
Uniprot ID:
P25594
Molecular weight:
50224.89844
General function:
Involved in transmembrane transport
Specific function:
Transporter required for vacuolar uptake of histidine, arginine and lysine and to a lesser extent tyrosine
Gene Name:
VBA2
Uniprot ID:
P38358
Molecular weight:
51676.39844
General function:
Involved in transport
Specific function:
High-affinity permease for lysine
Gene Name:
LYP1
Uniprot ID:
P32487
Molecular weight:
68089.10156